dbSNP rs1952224: SNHG31:n.351-40137G>A (chr2-214907688-G-A) – ACMG Classification: Benign (-10 pts)

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_ModerateBA1

The ENST00000607412.2(SNHG31):n.351-40137G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.39 in 152,074 control chromosomes in the GnomAD database, including 11,567 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.39 ( 11567 hom., cov: 33)

Consequence

SNHG31
ENST00000607412.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0480

Publications

4 publications found

Variant links:

Genes affected

SNHG31 (HGNC:54196): (small nucleolar RNA host gene 31)

SNHG31 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -10 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.26).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.388 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SNHG31	NR_110292.1 link	n.322-40137G>A		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
SNHG31	ENST00000607412.2 link	n.351-40137G>A	intron_variant	Intron 2 of 3	2
SNHG31	ENST00000655899.1 link	n.370-52705G>A	intron_variant	Intron 2 of 3
SNHG31	ENST00000664818.2 link	n.452-54122G>A	intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes

AF:

0.390

AC:

59245

AN:

151958

Hom.:

11557

Cov.:

show subpopulations

Gnomad AFR

AF:

0.371

Gnomad AMI

AF:

0.455

Gnomad AMR

AF:

0.396

Gnomad ASJ

AF:

0.491

Gnomad EAS

AF:

0.346

Gnomad SAS

AF:

0.387

Gnomad FIN

AF:

0.428

Gnomad MID

AF:

0.389

Gnomad NFE

AF:

0.391

Gnomad OTH

AF:

0.394

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome

AF:

0.390

AC:

59278

AN:

152074

Hom.:

11567

Cov.:

AF XY:

0.391

AC XY:

29057

AN XY:

74332

show subpopulations

African (AFR)

AF:

0.370

AC:

15372

AN:

41502

American (AMR)

AF:

0.397

AC:

6068

AN:

15294

Ashkenazi Jewish (ASJ)

AF:

0.491

AC:

1704

AN:

3472

East Asian (EAS)

AF:

0.346

AC:

1785

AN:

5152

South Asian (SAS)

AF:

0.386

AC:

1861

AN:

4824

European-Finnish (FIN)

AF:

0.428

AC:

4519

AN:

10548

Middle Eastern (MID)

AF:

0.405

AC:

119

AN:

294

European-Non Finnish (NFE)

AF:

0.391

AC:

26605

AN:

67966

Other (OTH)

AF:

0.393

AC:

830

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1907

3814

5721

7628

9535

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

572

1144

1716

2288

2860

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.394

Hom.:

6610

Bravo

AF:

0.384

Asia WGS

AF:

0.372

AC:

1291

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.26

CADD

Benign

(source)

DANN

Benign

0.65

PhyloP100

-0.048

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over